Dropped samples is often due to I/O buffer settings (and sometimes resource issues like ram, disk I/O or cpu), go to the menu bar and select "Adobe Audition"->Preferences...->"Audio Hardware". There is a setting drop down for "I/O Buffer Size". I think by default it's set to 512, you can try larger settings or smaller settings to see if this relieves the issue. I have good luck at 1024 on my Macbook Pro, but it's one of the later models and I have 4GB of ram and dual core CPU.
Another item that's helpful, is to try to set your audio hardware to the same sample rate of Audition. While Audition will convert on the fly, it's just a cleaner path and reduces a little extra processing.
As for Save/Export being grayed, this is a dumb question but does this happen when you have no files or sessions open? That is the only way I can get that to happen that I've seen, but curious if this is the case because if so, there is nothing to save or export, but once you have a file open or an MT session started then it will enable those options in the File menu.
I appreciate the time taken to provide a detailed reply, thank you!
Regarding greyed out Save/Export functions, it last happened when I had been processing a single track pre-recorded audio file and found after doing several edits and running some filters (mostly through Mac AU filters + AA3 noise reduction) that I couldn't save it. In the end I had to play the file and use another program to record what it played.
Thanks for the heads-up on the I/O Buffer Size. I'm running on a 2 GB (maxed) 2.16 GHz Intel Core 2 Duo MacBook.
Interesting point on the sample rate. For the external hardware I use (old Focusrite Saffire Firewire), I'll have to check it's default sampling rate...
I have not seen the export/save as options disabled except for the case where the active file was currently processing effects or edits. Otherwise, the menu options should always be enabled. Do you happen to recall some of the AU effects you might have been using at the time? I'd like to try to reproduce this problem.